gromacs: Upgrade biology/gromacs to 2019 release

This commit is contained in:
Jason Bacon 2019-02-04 13:14:39 -06:00
parent c8f445aa73
commit 5f8897b8ab
6 changed files with 779 additions and 0 deletions

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@ -1193,6 +1193,7 @@ SUBDIR+= gretl
SUBDIR+= greybird-theme
SUBDIR+= grilo-plugins
SUBDIR+= grisbi
SUBDIR+= gromacs
SUBDIR+= groovy
SUBDIR+= grpc-java
SUBDIR+= grsync

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gromacs/DESCR Normal file
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GROMACS is a versatile package to perform molecular dynamics,
i.e. simulate the Newtonian equations of motion for systems with
hundreds to millions of particles.
It is primarily designed for biochemical molecules like proteins,
lipids and nucleic acids that have a lot of complicated bonded
interactions, but since GROMACS is extremely fast at calculating
the nonbonded interactions (that usually dominate simulations)
many groups are also using it for research on non-biological
systems, e.g. polymers.

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gromacs/Makefile Normal file
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# $NetBSD: Makefile,v 1.17 2018/08/22 09:42:59 wiz Exp $
#
DISTNAME= gromacs-2019
CATEGORIES= science
MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/
MAINTAINER= bacon@NetBSD.org
HOMEPAGE= http://www.gromacs.org/
COMMENT= Molecular dynamics package
LICENSE= gnu-gpl-v2
USE_LANGUAGES= c c++
USE_TOOLS+= cmake pkg-config
USE_CMAKE= yes
.include "options.mk"
USE_TOOLS+= perl:run
REPLACE_PERL= scripts/demux.pl scripts/xplor2gmx.pl
CHECK_INTERPRETER_SKIP+= share/gromacs/tutor/gmxdemo/demo
.include "../../mk/bsd.prefs.mk"
.if $(MACHINE_ARCH) == "i386"
CFLAGS+= -msse -msse2
.endif
.include "../../math/fftw/buildlink3.mk"
.include "../../math/fftwf/buildlink3.mk"
.include "../../math/gsl/buildlink3.mk" # optional
.include "../../parallel/hwloc/buildlink3.mk"
.include "../../textproc/libxml2/buildlink3.mk" # optional
.include "../../mk/bsd.pkg.mk"

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gromacs/PLIST Normal file
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@comment $NetBSD$
bin/GMXRC
bin/GMXRC.bash
bin/GMXRC.csh
bin/GMXRC.zsh
bin/demux.pl
bin/gmx
bin/gmx-completion-gmx.bash
bin/gmx-completion.bash
bin/xplor2gmx.pl
include/gromacs/analysisdata.h
include/gromacs/analysisdata/abstractdata.h
include/gromacs/analysisdata/analysisdata.h
include/gromacs/analysisdata/arraydata.h
include/gromacs/analysisdata/dataframe.h
include/gromacs/analysisdata/datamodule.h
include/gromacs/analysisdata/modules/average.h
include/gromacs/analysisdata/modules/displacement.h
include/gromacs/analysisdata/modules/histogram.h
include/gromacs/analysisdata/modules/lifetime.h
include/gromacs/analysisdata/modules/plot.h
include/gromacs/commandline.h
include/gromacs/commandline/cmdlinehelpwriter.h
include/gromacs/commandline/cmdlineinit.h
include/gromacs/commandline/cmdlinemodule.h
include/gromacs/commandline/cmdlineoptionsmodule.h
include/gromacs/commandline/cmdlineparser.h
include/gromacs/commandline/cmdlineprogramcontext.h
include/gromacs/commandline/filenm.h
include/gromacs/commandline/pargs.h
include/gromacs/commandline/viewit.h
include/gromacs/compat/make_unique.h
include/gromacs/fft/fft.h
include/gromacs/fileio/confio.h
include/gromacs/fileio/enxio.h
include/gromacs/fileio/filetypes.h
include/gromacs/fileio/gmxfio.h
include/gromacs/fileio/matio.h
include/gromacs/fileio/mtxio.h
include/gromacs/fileio/oenv.h
include/gromacs/fileio/pdbio.h
include/gromacs/fileio/rgb.h
include/gromacs/fileio/tpxio.h
include/gromacs/fileio/trrio.h
include/gromacs/fileio/trxio.h
include/gromacs/fileio/xdr_datatype.h
include/gromacs/fileio/xtcio.h
include/gromacs/fileio/xvgr.h
include/gromacs/gmxana/gstat.h
include/gromacs/gpu_utils/hostallocator.h
include/gromacs/linearalgebra/eigensolver.h
include/gromacs/linearalgebra/matrix.h
include/gromacs/linearalgebra/sparsematrix.h
include/gromacs/math/3dtransforms.h
include/gromacs/math/arrayrefwithpadding.h
include/gromacs/math/do_fit.h
include/gromacs/math/functions.h
include/gromacs/math/gmxcomplex.h
include/gromacs/math/paddedvector.h
include/gromacs/math/units.h
include/gromacs/math/utilities.h
include/gromacs/math/vec.h
include/gromacs/math/vectypes.h
include/gromacs/mdlib/simulationsignal.h
include/gromacs/mdtypes/inputrec.h
include/gromacs/mdtypes/md_enums.h
include/gromacs/mdtypes/mdatom.h
include/gromacs/mdtypes/state.h
include/gromacs/options.h
include/gromacs/options/abstractoption.h
include/gromacs/options/abstractsection.h
include/gromacs/options/basicoptions.h
include/gromacs/options/filenameoption.h
include/gromacs/options/filenameoptionmanager.h
include/gromacs/options/ioptionsbehavior.h
include/gromacs/options/ioptionscontainer.h
include/gromacs/options/ioptionscontainerwithsections.h
include/gromacs/options/isectionstorage.h
include/gromacs/options/ivaluestore.h
include/gromacs/options/optionfiletype.h
include/gromacs/options/optionflags.h
include/gromacs/options/options.h
include/gromacs/options/optionsection.h
include/gromacs/options/repeatingsection.h
include/gromacs/options/timeunitmanager.h
include/gromacs/options/valuestore.h
include/gromacs/pbcutil/ishift.h
include/gromacs/pbcutil/pbc.h
include/gromacs/pbcutil/rmpbc.h
include/gromacs/random.h
include/gromacs/random/exponentialdistribution.h
include/gromacs/random/gammadistribution.h
include/gromacs/random/normaldistribution.h
include/gromacs/random/seed.h
include/gromacs/random/tabulatednormaldistribution.h
include/gromacs/random/threefry.h
include/gromacs/random/uniformintdistribution.h
include/gromacs/random/uniformrealdistribution.h
include/gromacs/restraint/restraintpotential.h
include/gromacs/selection.h
include/gromacs/selection/indexutil.h
include/gromacs/selection/nbsearch.h
include/gromacs/selection/position.h
include/gromacs/selection/selection.h
include/gromacs/selection/selectioncollection.h
include/gromacs/selection/selectionenums.h
include/gromacs/selection/selectionoption.h
include/gromacs/selection/selectionoptionbehavior.h
include/gromacs/selection/selectionoptionmanager.h
include/gromacs/timing/wallcycle.h
include/gromacs/timing/walltime_accounting.h
include/gromacs/topology/atomprop.h
include/gromacs/topology/atoms.h
include/gromacs/topology/block.h
include/gromacs/topology/forcefieldparameters.h
include/gromacs/topology/idef.h
include/gromacs/topology/ifunc.h
include/gromacs/topology/index.h
include/gromacs/topology/mtop_util.h
include/gromacs/topology/symtab.h
include/gromacs/topology/topology.h
include/gromacs/trajectory/energyframe.h
include/gromacs/trajectory/trajectoryframe.h
include/gromacs/trajectoryanalysis.h
include/gromacs/trajectoryanalysis/analysismodule.h
include/gromacs/trajectoryanalysis/analysissettings.h
include/gromacs/trajectoryanalysis/cmdlinerunner.h
include/gromacs/trajectoryanalysis/topologyinformation.h
include/gromacs/utility.h
include/gromacs/utility/alignedallocator.h
include/gromacs/utility/allocator.h
include/gromacs/utility/arrayref.h
include/gromacs/utility/arraysize.h
include/gromacs/utility/basedefinitions.h
include/gromacs/utility/baseversion.h
include/gromacs/utility/classhelpers.h
include/gromacs/utility/cstringutil.h
include/gromacs/utility/current_function.h
include/gromacs/utility/datafilefinder.h
include/gromacs/utility/errorcodes.h
include/gromacs/utility/exceptions.h
include/gromacs/utility/fatalerror.h
include/gromacs/utility/fileptr.h
include/gromacs/utility/flags.h
include/gromacs/utility/futil.h
include/gromacs/utility/gmxassert.h
include/gromacs/utility/init.h
include/gromacs/utility/programcontext.h
include/gromacs/utility/real.h
include/gromacs/utility/smalloc.h
include/gromacs/utility/stringutil.h
include/gromacs/utility/unique_cptr.h
include/gromacs/version.h
lib/libgromacs.so
lib/libgromacs.so.4
lib/libgromacs.so.4.0.0
lib/pkgconfig/libgromacs.pc
man/man1/gmx-anadock.1
man/man1/gmx-anaeig.1
man/man1/gmx-analyze.1
man/man1/gmx-angle.1
man/man1/gmx-awh.1
man/man1/gmx-bar.1
man/man1/gmx-bundle.1
man/man1/gmx-check.1
man/man1/gmx-chi.1
man/man1/gmx-cluster.1
man/man1/gmx-clustsize.1
man/man1/gmx-confrms.1
man/man1/gmx-convert-tpr.1
man/man1/gmx-covar.1
man/man1/gmx-current.1
man/man1/gmx-density.1
man/man1/gmx-densmap.1
man/man1/gmx-densorder.1
man/man1/gmx-dielectric.1
man/man1/gmx-dipoles.1
man/man1/gmx-disre.1
man/man1/gmx-distance.1
man/man1/gmx-do_dssp.1
man/man1/gmx-dos.1
man/man1/gmx-dump.1
man/man1/gmx-dyecoupl.1
man/man1/gmx-dyndom.1
man/man1/gmx-editconf.1
man/man1/gmx-eneconv.1
man/man1/gmx-enemat.1
man/man1/gmx-energy.1
man/man1/gmx-filter.1
man/man1/gmx-freevolume.1
man/man1/gmx-gangle.1
man/man1/gmx-genconf.1
man/man1/gmx-genion.1
man/man1/gmx-genrestr.1
man/man1/gmx-grompp.1
man/man1/gmx-gyrate.1
man/man1/gmx-h2order.1
man/man1/gmx-hbond.1
man/man1/gmx-helix.1
man/man1/gmx-helixorient.1
man/man1/gmx-help.1
man/man1/gmx-hydorder.1
man/man1/gmx-insert-molecules.1
man/man1/gmx-lie.1
man/man1/gmx-make_edi.1
man/man1/gmx-make_ndx.1
man/man1/gmx-mdmat.1
man/man1/gmx-mdrun.1
man/man1/gmx-mindist.1
man/man1/gmx-mk_angndx.1
man/man1/gmx-morph.1
man/man1/gmx-msd.1
man/man1/gmx-nmeig.1
man/man1/gmx-nmens.1
man/man1/gmx-nmr.1
man/man1/gmx-nmtraj.1
man/man1/gmx-order.1
man/man1/gmx-pairdist.1
man/man1/gmx-pdb2gmx.1
man/man1/gmx-pme_error.1
man/man1/gmx-polystat.1
man/man1/gmx-potential.1
man/man1/gmx-principal.1
man/man1/gmx-rama.1
man/man1/gmx-rdf.1
man/man1/gmx-report-methods.1
man/man1/gmx-rms.1
man/man1/gmx-rmsdist.1
man/man1/gmx-rmsf.1
man/man1/gmx-rotacf.1
man/man1/gmx-rotmat.1
man/man1/gmx-saltbr.1
man/man1/gmx-sans.1
man/man1/gmx-sasa.1
man/man1/gmx-saxs.1
man/man1/gmx-select.1
man/man1/gmx-sham.1
man/man1/gmx-sigeps.1
man/man1/gmx-solvate.1
man/man1/gmx-sorient.1
man/man1/gmx-spatial.1
man/man1/gmx-spol.1
man/man1/gmx-tcaf.1
man/man1/gmx-traj.1
man/man1/gmx-trajectory.1
man/man1/gmx-trjcat.1
man/man1/gmx-trjconv.1
man/man1/gmx-trjorder.1
man/man1/gmx-tune_pme.1
man/man1/gmx-vanhove.1
man/man1/gmx-velacc.1
man/man1/gmx-view.1
man/man1/gmx-wham.1
man/man1/gmx-wheel.1
man/man1/gmx-x2top.1
man/man1/gmx-xpm2ps.1
man/man1/gmx.1
share/cmake/gromacs/gromacs-config-version.cmake
share/cmake/gromacs/gromacs-config.cmake
share/cmake/gromacs/libgromacs-release.cmake
share/cmake/gromacs/libgromacs.cmake
share/gromacs/COPYING
share/gromacs/README.tutor
share/gromacs/README_FreeEnergyModifications.txt
share/gromacs/template/CMakeLists.txt
share/gromacs/template/Makefile.pkg
share/gromacs/template/README
share/gromacs/template/cmake/FindGROMACS.cmake
share/gromacs/template/template.cpp
share/gromacs/top/README
share/gromacs/top/amber03.ff/aminoacids.arn
share/gromacs/top/amber03.ff/aminoacids.c.tdb
share/gromacs/top/amber03.ff/aminoacids.hdb
share/gromacs/top/amber03.ff/aminoacids.n.tdb
share/gromacs/top/amber03.ff/aminoacids.r2b
share/gromacs/top/amber03.ff/aminoacids.rtp
share/gromacs/top/amber03.ff/aminoacids.vsd
share/gromacs/top/amber03.ff/atomtypes.atp
share/gromacs/top/amber03.ff/dna.arn
share/gromacs/top/amber03.ff/dna.hdb
share/gromacs/top/amber03.ff/dna.r2b
share/gromacs/top/amber03.ff/dna.rtp
share/gromacs/top/amber03.ff/ffbonded.itp
share/gromacs/top/amber03.ff/ffnonbonded.itp
share/gromacs/top/amber03.ff/forcefield.doc
share/gromacs/top/amber03.ff/forcefield.itp
share/gromacs/top/amber03.ff/ions.itp
share/gromacs/top/amber03.ff/rna.arn
share/gromacs/top/amber03.ff/rna.hdb
share/gromacs/top/amber03.ff/rna.r2b
share/gromacs/top/amber03.ff/rna.rtp
share/gromacs/top/amber03.ff/spc.itp
share/gromacs/top/amber03.ff/spce.itp
share/gromacs/top/amber03.ff/tip3p.itp
share/gromacs/top/amber03.ff/tip4p.itp
share/gromacs/top/amber03.ff/tip4pew.itp
share/gromacs/top/amber03.ff/tip5p.itp
share/gromacs/top/amber03.ff/urea.itp
share/gromacs/top/amber03.ff/watermodels.dat
share/gromacs/top/amber94.ff/aminoacids.arn
share/gromacs/top/amber94.ff/aminoacids.c.tdb
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share/gromacs/top/amber94.ff/aminoacids.n.tdb
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share/gromacs/top/amber94.ff/aminoacids.vsd
share/gromacs/top/amber94.ff/atomtypes.atp
share/gromacs/top/amber94.ff/dna.arn
share/gromacs/top/amber94.ff/dna.hdb
share/gromacs/top/amber94.ff/dna.r2b
share/gromacs/top/amber94.ff/dna.rtp
share/gromacs/top/amber94.ff/ffbonded.itp
share/gromacs/top/amber94.ff/ffnonbonded.itp
share/gromacs/top/amber94.ff/forcefield.doc
share/gromacs/top/amber94.ff/forcefield.itp
share/gromacs/top/amber94.ff/ions.itp
share/gromacs/top/amber94.ff/rna.arn
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share/gromacs/top/amber96.ff/aminoacids.arn
share/gromacs/top/amber96.ff/aminoacids.c.tdb
share/gromacs/top/amber96.ff/aminoacids.hdb
share/gromacs/top/amber96.ff/aminoacids.n.tdb
share/gromacs/top/amber96.ff/aminoacids.r2b
share/gromacs/top/amber96.ff/aminoacids.rtp
share/gromacs/top/amber96.ff/aminoacids.vsd
share/gromacs/top/amber96.ff/atomtypes.atp
share/gromacs/top/amber96.ff/dna.arn
share/gromacs/top/amber96.ff/dna.hdb
share/gromacs/top/amber96.ff/dna.r2b
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share/gromacs/top/amber99sb-ildn.ff/rna.rtp
share/gromacs/top/amber99sb-ildn.ff/spc.itp
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share/gromacs/top/amber99sb-ildn.ff/tip5p.itp
share/gromacs/top/amber99sb-ildn.ff/urea.itp
share/gromacs/top/amber99sb-ildn.ff/watermodels.dat
share/gromacs/top/amber99sb.ff/aminoacids.arn
share/gromacs/top/amber99sb.ff/aminoacids.c.tdb
share/gromacs/top/amber99sb.ff/aminoacids.hdb
share/gromacs/top/amber99sb.ff/aminoacids.n.tdb
share/gromacs/top/amber99sb.ff/aminoacids.r2b
share/gromacs/top/amber99sb.ff/aminoacids.rtp
share/gromacs/top/amber99sb.ff/aminoacids.vsd
share/gromacs/top/amber99sb.ff/atomtypes.atp
share/gromacs/top/amber99sb.ff/dna.arn
share/gromacs/top/amber99sb.ff/dna.hdb
share/gromacs/top/amber99sb.ff/dna.r2b
share/gromacs/top/amber99sb.ff/dna.rtp
share/gromacs/top/amber99sb.ff/ffbonded.itp
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share/gromacs/top/amber99sb.ff/ions.itp
share/gromacs/top/amber99sb.ff/rna.arn
share/gromacs/top/amber99sb.ff/rna.hdb
share/gromacs/top/amber99sb.ff/rna.r2b
share/gromacs/top/amber99sb.ff/rna.rtp
share/gromacs/top/amber99sb.ff/spc.itp
share/gromacs/top/amber99sb.ff/spce.itp
share/gromacs/top/amber99sb.ff/tip3p.itp
share/gromacs/top/amber99sb.ff/tip4p.itp
share/gromacs/top/amber99sb.ff/tip4pew.itp
share/gromacs/top/amber99sb.ff/tip5p.itp
share/gromacs/top/amber99sb.ff/urea.itp
share/gromacs/top/amber99sb.ff/watermodels.dat
share/gromacs/top/amberGS.ff/aminoacids.arn
share/gromacs/top/amberGS.ff/aminoacids.c.tdb
share/gromacs/top/amberGS.ff/aminoacids.hdb
share/gromacs/top/amberGS.ff/aminoacids.n.tdb
share/gromacs/top/amberGS.ff/aminoacids.r2b
share/gromacs/top/amberGS.ff/aminoacids.rtp
share/gromacs/top/amberGS.ff/aminoacids.vsd
share/gromacs/top/amberGS.ff/atomtypes.atp
share/gromacs/top/amberGS.ff/dna.arn
share/gromacs/top/amberGS.ff/dna.hdb
share/gromacs/top/amberGS.ff/dna.r2b
share/gromacs/top/amberGS.ff/dna.rtp
share/gromacs/top/amberGS.ff/ffbonded.itp
share/gromacs/top/amberGS.ff/ffnonbonded.itp
share/gromacs/top/amberGS.ff/forcefield.doc
share/gromacs/top/amberGS.ff/forcefield.itp
share/gromacs/top/amberGS.ff/ions.itp
share/gromacs/top/amberGS.ff/rna.arn
share/gromacs/top/amberGS.ff/rna.hdb
share/gromacs/top/amberGS.ff/rna.r2b
share/gromacs/top/amberGS.ff/rna.rtp
share/gromacs/top/amberGS.ff/spc.itp
share/gromacs/top/amberGS.ff/spce.itp
share/gromacs/top/amberGS.ff/tip3p.itp
share/gromacs/top/amberGS.ff/tip4p.itp
share/gromacs/top/amberGS.ff/tip4pew.itp
share/gromacs/top/amberGS.ff/tip5p.itp
share/gromacs/top/amberGS.ff/urea.itp
share/gromacs/top/amberGS.ff/watermodels.dat
share/gromacs/top/atom_nom.tbl
share/gromacs/top/atommass.dat
share/gromacs/top/bonds.dlg
share/gromacs/top/ca-shift.dat
share/gromacs/top/cb-shift.dat
share/gromacs/top/charmm27.ff/aminoacids.arn
share/gromacs/top/charmm27.ff/aminoacids.c.tdb
share/gromacs/top/charmm27.ff/aminoacids.hdb
share/gromacs/top/charmm27.ff/aminoacids.n.tdb
share/gromacs/top/charmm27.ff/aminoacids.r2b
share/gromacs/top/charmm27.ff/aminoacids.rtp
share/gromacs/top/charmm27.ff/aminoacids.vsd
share/gromacs/top/charmm27.ff/atomtypes.atp
share/gromacs/top/charmm27.ff/cmap.itp
share/gromacs/top/charmm27.ff/dna.arn
share/gromacs/top/charmm27.ff/dna.c.tdb
share/gromacs/top/charmm27.ff/dna.hdb
share/gromacs/top/charmm27.ff/dna.n.tdb
share/gromacs/top/charmm27.ff/dna.rtp
share/gromacs/top/charmm27.ff/ffbonded.itp
share/gromacs/top/charmm27.ff/ffnabonded.itp
share/gromacs/top/charmm27.ff/ffnanonbonded.itp
share/gromacs/top/charmm27.ff/ffnonbonded.itp
share/gromacs/top/charmm27.ff/forcefield.doc
share/gromacs/top/charmm27.ff/forcefield.itp
share/gromacs/top/charmm27.ff/ions.itp
share/gromacs/top/charmm27.ff/lipids.hdb
share/gromacs/top/charmm27.ff/lipids.rtp
share/gromacs/top/charmm27.ff/rna.arn
share/gromacs/top/charmm27.ff/rna.c.tdb
share/gromacs/top/charmm27.ff/rna.hdb
share/gromacs/top/charmm27.ff/rna.n.tdb
share/gromacs/top/charmm27.ff/rna.r2b
share/gromacs/top/charmm27.ff/rna.rtp
share/gromacs/top/charmm27.ff/spc.itp
share/gromacs/top/charmm27.ff/spce.itp
share/gromacs/top/charmm27.ff/tip3p.itp
share/gromacs/top/charmm27.ff/tip4p.itp
share/gromacs/top/charmm27.ff/tip5p.itp
share/gromacs/top/charmm27.ff/tips3p.itp
share/gromacs/top/charmm27.ff/watermodels.dat
share/gromacs/top/co-shift.dat
share/gromacs/top/defselection.dat
share/gromacs/top/dgsolv.dat
share/gromacs/top/edissoc.dat
share/gromacs/top/electroneg.dat
share/gromacs/top/elements.dat
share/gromacs/top/export.dlg
share/gromacs/top/ffG43a1.itp
share/gromacs/top/ffG43a2.itp
share/gromacs/top/ffG45a3.itp
share/gromacs/top/ffG53a5.itp
share/gromacs/top/ffG53a6.itp
share/gromacs/top/ffoplsaa-n.tst
share/gromacs/top/ffoplsaa.itp
share/gromacs/top/flexspc.itp
share/gromacs/top/flexspce.itp
share/gromacs/top/flexwat-ferguson.itp
share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb
share/gromacs/top/gromos43a1.ff/aminoacids.hdb
share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb
share/gromacs/top/gromos43a1.ff/aminoacids.r2b
share/gromacs/top/gromos43a1.ff/aminoacids.rtp
share/gromacs/top/gromos43a1.ff/aminoacids.vsd
share/gromacs/top/gromos43a1.ff/atomtypes.atp
share/gromacs/top/gromos43a1.ff/ff_dum.itp
share/gromacs/top/gromos43a1.ff/ffbonded.itp
share/gromacs/top/gromos43a1.ff/ffnonbonded.itp
share/gromacs/top/gromos43a1.ff/forcefield.doc
share/gromacs/top/gromos43a1.ff/forcefield.itp
share/gromacs/top/gromos43a1.ff/ions.itp
share/gromacs/top/gromos43a1.ff/methanol.itp
share/gromacs/top/gromos43a1.ff/methanol216.gro
share/gromacs/top/gromos43a1.ff/spc.itp
share/gromacs/top/gromos43a1.ff/spce.itp
share/gromacs/top/gromos43a1.ff/tip3p.itp
share/gromacs/top/gromos43a1.ff/tip4p.itp
share/gromacs/top/gromos43a1.ff/watermodels.dat
share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb
share/gromacs/top/gromos43a2.ff/aminoacids.hdb
share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb
share/gromacs/top/gromos43a2.ff/aminoacids.r2b
share/gromacs/top/gromos43a2.ff/aminoacids.rtp
share/gromacs/top/gromos43a2.ff/aminoacids.vsd
share/gromacs/top/gromos43a2.ff/atomtypes.atp
share/gromacs/top/gromos43a2.ff/ff_dum.itp
share/gromacs/top/gromos43a2.ff/ffbonded.itp
share/gromacs/top/gromos43a2.ff/ffnonbonded.itp
share/gromacs/top/gromos43a2.ff/forcefield.doc
share/gromacs/top/gromos43a2.ff/forcefield.itp
share/gromacs/top/gromos43a2.ff/ions.itp
share/gromacs/top/gromos43a2.ff/spc.itp
share/gromacs/top/gromos43a2.ff/spce.itp
share/gromacs/top/gromos43a2.ff/tip3p.itp
share/gromacs/top/gromos43a2.ff/tip4p.itp
share/gromacs/top/gromos43a2.ff/watermodels.dat
share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb
share/gromacs/top/gromos45a3.ff/aminoacids.hdb
share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb
share/gromacs/top/gromos45a3.ff/aminoacids.r2b
share/gromacs/top/gromos45a3.ff/aminoacids.rtp
share/gromacs/top/gromos45a3.ff/aminoacids.vsd
share/gromacs/top/gromos45a3.ff/atomtypes.atp
share/gromacs/top/gromos45a3.ff/ff_dum.itp
share/gromacs/top/gromos45a3.ff/ffbonded.itp
share/gromacs/top/gromos45a3.ff/ffnonbonded.itp
share/gromacs/top/gromos45a3.ff/forcefield.doc
share/gromacs/top/gromos45a3.ff/forcefield.itp
share/gromacs/top/gromos45a3.ff/ions.itp
share/gromacs/top/gromos45a3.ff/spc.itp
share/gromacs/top/gromos45a3.ff/spce.itp
share/gromacs/top/gromos45a3.ff/tip3p.itp
share/gromacs/top/gromos45a3.ff/tip4p.itp
share/gromacs/top/gromos45a3.ff/watermodels.dat
share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb
share/gromacs/top/gromos53a5.ff/aminoacids.hdb
share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb
share/gromacs/top/gromos53a5.ff/aminoacids.r2b
share/gromacs/top/gromos53a5.ff/aminoacids.rtp
share/gromacs/top/gromos53a5.ff/aminoacids.vsd
share/gromacs/top/gromos53a5.ff/atomname2type.n2t
share/gromacs/top/gromos53a5.ff/atomtypes.atp
share/gromacs/top/gromos53a5.ff/ff_dum.itp
share/gromacs/top/gromos53a5.ff/ffbonded.itp
share/gromacs/top/gromos53a5.ff/ffnonbonded.itp
share/gromacs/top/gromos53a5.ff/forcefield.doc
share/gromacs/top/gromos53a5.ff/forcefield.itp
share/gromacs/top/gromos53a5.ff/ions.itp
share/gromacs/top/gromos53a5.ff/spc.itp
share/gromacs/top/gromos53a5.ff/spce.itp
share/gromacs/top/gromos53a5.ff/tip3p.itp
share/gromacs/top/gromos53a5.ff/tip4p.itp
share/gromacs/top/gromos53a5.ff/watermodels.dat
share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
share/gromacs/top/gromos53a6.ff/aminoacids.hdb
share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
share/gromacs/top/gromos53a6.ff/aminoacids.r2b
share/gromacs/top/gromos53a6.ff/aminoacids.rtp
share/gromacs/top/gromos53a6.ff/aminoacids.vsd
share/gromacs/top/gromos53a6.ff/atomtypes.atp
share/gromacs/top/gromos53a6.ff/ff_dum.itp
share/gromacs/top/gromos53a6.ff/ffbonded.itp
share/gromacs/top/gromos53a6.ff/ffnonbonded.itp
share/gromacs/top/gromos53a6.ff/forcefield.doc
share/gromacs/top/gromos53a6.ff/forcefield.itp
share/gromacs/top/gromos53a6.ff/ions.itp
share/gromacs/top/gromos53a6.ff/spc.itp
share/gromacs/top/gromos53a6.ff/spce.itp
share/gromacs/top/gromos53a6.ff/tip3p.itp
share/gromacs/top/gromos53a6.ff/tip4p.itp
share/gromacs/top/gromos53a6.ff/watermodels.dat
share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb
share/gromacs/top/gromos54a7.ff/aminoacids.hdb
share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb
share/gromacs/top/gromos54a7.ff/aminoacids.r2b
share/gromacs/top/gromos54a7.ff/aminoacids.rtp
share/gromacs/top/gromos54a7.ff/aminoacids.vsd
share/gromacs/top/gromos54a7.ff/atomtypes.atp
share/gromacs/top/gromos54a7.ff/dppc.itp
share/gromacs/top/gromos54a7.ff/ff_dum.itp
share/gromacs/top/gromos54a7.ff/ffbonded.itp
share/gromacs/top/gromos54a7.ff/ffnonbonded.itp
share/gromacs/top/gromos54a7.ff/forcefield.doc
share/gromacs/top/gromos54a7.ff/forcefield.itp
share/gromacs/top/gromos54a7.ff/ions.itp
share/gromacs/top/gromos54a7.ff/popc.itp
share/gromacs/top/gromos54a7.ff/spc.itp
share/gromacs/top/gromos54a7.ff/spce.itp
share/gromacs/top/gromos54a7.ff/tip3p.itp
share/gromacs/top/gromos54a7.ff/tip4p.itp
share/gromacs/top/gromos54a7.ff/tmcl.itp
share/gromacs/top/gromos54a7.ff/watermodels.dat
share/gromacs/top/ha-shift.dat
share/gromacs/top/ions.itp
share/gromacs/top/nsfactor.dat
share/gromacs/top/oplsaa.ff/1propanol.itp
share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
share/gromacs/top/oplsaa.ff/aminoacids.hdb
share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
share/gromacs/top/oplsaa.ff/aminoacids.r2b
share/gromacs/top/oplsaa.ff/aminoacids.rtp
share/gromacs/top/oplsaa.ff/aminoacids.vsd
share/gromacs/top/oplsaa.ff/atomname2type.n2t
share/gromacs/top/oplsaa.ff/atomtypes.atp
share/gromacs/top/oplsaa.ff/ethanol.itp
share/gromacs/top/oplsaa.ff/ffbonded.itp
share/gromacs/top/oplsaa.ff/ffnonbonded.itp
share/gromacs/top/oplsaa.ff/forcefield.doc
share/gromacs/top/oplsaa.ff/forcefield.itp
share/gromacs/top/oplsaa.ff/ions.itp
share/gromacs/top/oplsaa.ff/methanol.itp
share/gromacs/top/oplsaa.ff/spc.itp
share/gromacs/top/oplsaa.ff/spce.itp
share/gromacs/top/oplsaa.ff/tip3p.itp
share/gromacs/top/oplsaa.ff/tip4p.itp
share/gromacs/top/oplsaa.ff/tip4pew.itp
share/gromacs/top/oplsaa.ff/tip5p.itp
share/gromacs/top/oplsaa.ff/tip5pe.itp
share/gromacs/top/oplsaa.ff/watermodels.dat
share/gromacs/top/phbres.dat
share/gromacs/top/ps.m2p
share/gromacs/top/random.dat
share/gromacs/top/refi_aa.dat
share/gromacs/top/residues.dtd
share/gromacs/top/residues.xml
share/gromacs/top/residuetypes.dat
share/gromacs/top/sfactor.dat
share/gromacs/top/spc.itp
share/gromacs/top/spc216.gro
share/gromacs/top/spce.itp
share/gromacs/top/specbond.dat
share/gromacs/top/ss.map
share/gromacs/top/surface.dat
share/gromacs/top/sw.itp
share/gromacs/top/table6-10.xvg
share/gromacs/top/table6-11.xvg
share/gromacs/top/table6-12.xvg
share/gromacs/top/table6-8.xvg
share/gromacs/top/table6-9.xvg
share/gromacs/top/tip3p.itp
share/gromacs/top/tip4p.gro
share/gromacs/top/tip4p.itp
share/gromacs/top/tip5p.gro
share/gromacs/top/vdw-msms.dat
share/gromacs/top/vdwradii.dat
share/gromacs/top/xlateat.dat

6
gromacs/distinfo Normal file
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@ -0,0 +1,6 @@
$NetBSD$
SHA1 (gromacs-2019.tar.gz) = 89155f31489be22593b98d403113d5eb5881a792
RMD160 (gromacs-2019.tar.gz) = 598f0b3b797a801ff5b4acef38cc248f69656fc2
SHA512 (gromacs-2019.tar.gz) = 54b11530e8ff671461e3ae9418d991fe242957943c944798cddf6efe740eee670a562cd5201dbba68b045f4bafd3afa2dc8de27e0643c7def4e05eaf0ccb5769
Size (gromacs-2019.tar.gz) = 33428725 bytes

28
gromacs/options.mk Normal file
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# $NetBSD: options.mk,v 1.2 2010/05/16 12:04:03 asau Exp $
PKG_OPTIONS_VAR= PKG_OPTIONS.gromacs
PKG_SUPPORTED_OPTIONS+= mpi x11
PKG_SUGGESTED_OPTIONS+= mpi x11
.include "../../mk/bsd.options.mk"
PLIST_VARS= x11
# MPI support:
.if !empty(PKG_OPTIONS:Mmpi)
CONFIGURE_ARGS+= --enable-mpi
PLIST_SUBST+= MPI=_mpi
.include "../../mk/mpi.buildlink3.mk"
.else
PLIST_SUBST+= MPI=
.endif
# X support:
.if !empty(PKG_OPTIONS:Mx11)
CONFIGURE_ARGS+= --with-x
PLIST.x11= yes
.include "../../x11/libX11/buildlink3.mk"
.include "../../x11/libICE/buildlink3.mk"
.include "../../x11/libSM/buildlink3.mk"
.endif